Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_028314083.1 G491_RS0107090 2-isopropylmalate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_000429905.1:WP_028314083.1 Length = 516 Score = 374 bits (961), Expect = e-108 Identities = 212/498 (42%), Positives = 304/498 (61%), Gaps = 16/498 (3%) Query: 2 QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61 +V + DTTLRDGEQ+PG ++ +EK+RIA +++ALG DI+EAG SEG+ ++ + + Sbjct: 4 RVYIFDTTLRDGEQSPGATMNAKEKVRIASRLEALGVDIMEAGFPAASEGDFAAVQDVAA 63 Query: 62 EGLRAEICSFARAVREDIDAAISCDVDS----VHLVVPTSDLHLEHKLRKTREEVLEQAV 117 ++ + AR + DID A + +H + TSD+HLEHKL+ RE+V+E AV Sbjct: 64 VCQKSSVAGLARTSKSDIDKAWGAVQHAKHPRIHTFIATSDIHLEHKLKMNREQVVEAAV 123 Query: 118 DCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYEF 177 + +YA VE SAED +RSD D+L +F I AGA + DTVG P E Sbjct: 124 NAVKYAKSFTDDVEFSAEDGSRSDRDYLCRVFEAAIAAGATTVNLPDTVGYAIPHEFAEL 183 Query: 178 YRGLSELG-----APLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEE 232 + + + A LSVHCHND GLA +N+LA ++AGA + T+NGIGERAGN +LEE Sbjct: 184 VKYVMDHTPNIHQAILSVHCHNDLGLATSNTLAAIQAGARQAEVTVNGIGERAGNTSLEE 243 Query: 233 VVVALKS---LYDVDTSINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADG 289 VV+A+ + D T+I E ++ SR+V +TG+ +QPNKAIVG NAFAHE+GIH DG Sbjct: 244 VVMAMHTRPNYLDFHTNIVTEQIHPASRLVRMITGIMVQPNKAIVGANAFAHEAGIHQDG 303 Query: 290 VLKKAETYEPITPEMVGHGR-GFVMGKHIGTHALRKRLDELGMKVADDKLMEIFRRVKTL 348 VLK TYE + PE VG + V+GKH G HALR L ++G ++D++L ++F + K L Sbjct: 304 VLKNPMTYEIMRPETVGLSKNNMVLGKHSGRHALRSHLADMGYVLSDEELQDLFIKFKDL 363 Query: 349 GDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPTASVKLRVDDREVLEAG 408 D K V D DL+A+ + DK L + + +G V PTA+V L+ + ++ A Sbjct: 364 ADKKKHVVDEDLEALVSIGILRTSDK-YSLDYLHVSAGTGVKPTATVGLKTNGDVLMGAE 422 Query: 409 TGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVIKLRHGDRIISARSTQ 468 G GP+DAA I K +++ + V A+TGGTDA +V ++L+ G I R Sbjct: 423 FGNGPIDAAFNTIAKMTGTTSEML--RFTVSALTGGTDAQGEVTVRLQEGKNIALGRGVD 480 Query: 469 PDIIMASVEAFLSGVNRL 486 PDII AS +A+++G+NRL Sbjct: 481 PDIITASAKAYVNGINRL 498 Lambda K H 0.317 0.135 0.373 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 656 Number of extensions: 34 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 496 Length of database: 516 Length adjustment: 34 Effective length of query: 462 Effective length of database: 482 Effective search space: 222684 Effective search space used: 222684 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory